Track Sources for outputs with BIDS URIs

[tsalo]

Closes #568.

Breaking changes

• Don't write out the temporal mask if fd_thresh is <= 0 (i.e., censoring is disabled).
• Don't write out design file if params is None (i.e., denoising is disabled).

Changes proposed in this pull request

• Plug BIDS URIs into appropriate JSON files with the Sources field.
• Also add in a number of metadata fields required or recommended by BEP 012 (BEP 012: Functional MRI derivatives bids-standard/bids-specification#519).
• Add DatasetLinks field to dataset description file. The links are to the preprocessed data, the XCP-D derivatives, and (optionally) the custom confounds.
• Create a series of small functions (listed below) to generate BIDS URIs for different file locations:
  • _make_uri: General path-resolving function.
  • _make_xcpd_uri: Resolves path for XCP-D derivative files.
  • _make_xcpd_uri_lol: Resolves path for XCP-D derivative files organized in lists of lists..
  • _make_preproc_uri: Resolves path for preprocessing pipeline derivative files.
  • _make_custom_uri: Resolves path for custom confounds files.
• Create some functions that help with managing the Sources field in workflows.
  • _listify: From NiMARE. Convert things to lists.
  • _make_dictionary: Feed kwargs into a dictionary. I use this to create metadata dictionaries containing Sources fields to pass into DerivativesDataSinks. The issue is that MapNodes need to reference fields in the .inputs attribute of the underlying interface, but DerivativesDataSinks don't include Sources as a field in .inputs. However, they do include meta_dict, so I need to pass in a meta_dict containing the Sources field instead of passing in Sources directly.
  • _transpose_lol: Transposes a list of lists. Used in _make_xcpd_uri_lol.

[tsalo]

The concatenated atlas-wise sources aren't right. Instead of selecting the appropriate atlas's element in the run-wise lists of sources, it's just keeping the full run-wise lists.

[codecov]

Codecov Report

Attention: 11 lines in your changes are missing coverage. Please review.

Files	Coverage Δ
xcp_d/utils/bids.py	88.50% <100.00%> (+1.62%)	⬆️
xcp_d/workflows/base.py	97.12% <ø> (ø)
xcp_d/workflows/bold.py	94.36% <ø> (ø)
xcp_d/workflows/cifti.py	93.65% <ø> (ø)
xcp_d/workflows/connectivity.py	97.00% <100.00%> (ø)
xcp_d/utils/utils.py	98.81% <88.23%> (-1.19%)	⬇️
xcp_d/workflows/concatenation.py	88.46% <77.77%> (+1.22%)	⬆️
xcp_d/workflows/outputs.py	92.03% <90.41%> (+4.80%)	⬆️

📢 Thoughts on this report? Let us know!.

[tsalo]

@mattcieslak would you mind reviewing this with an eye toward streamlining the code? I'm sure I'll be able to improve it over time, but if there's anything obvious that I'm missing it would be great to catch it before I merge the PR.

[tsalo]

Whoops, looks like the add-coverage-to-sources step is overwriting the sources without retaining the old ones. I'll need to figure out what went wrong with my recent changes before merging.

EDIT: Fixed!